Abstract

Exposure of newborns to the maternal vaginal microbiota is interrupted with cesarean birthing. Babies delivered by cesarean section (C-section) acquire a microbiota that differs from that of vaginally delivered infants, and C-section delivery has been associated with increased risk for immune and metabolic disorders. Here we conducted a pilot study in which infants delivered by C-section were exposed to maternal vaginal fluids at birth. Similarly to vaginally delivered babies, the gut, oral and skin bacterial communities of these newborns during the first 30 d of life was enriched in vaginal bacteria—which were underrepresented in unexposed C-section–delivered infants—and the microbiome similarity to those of vaginally delivered infants was greater in oral and skin samples than in anal samples. Although the long-term health consequences of restoring the microbiota of C-section–delivered infants remain unclear, our results demonstrate that vaginal microbes can be partially restored at birth in C-section–delivered babies.

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Acknowledgements

This work was partially supported by the C&D Research Fund (M.G.D.-B.), the US National Institutes of Health grant no. R01 DK090989 (M.G.D.-B), the Crohn's and Colitis Foundation of America grant no. 362048 (J.C.C.) and the Sinai Ulcerative Colitis: Clinical, Experimental & Systems Studies philanthropic grant (J.C.C.). Sequencing at the New York University Genome Technology Center was partially supported by the Cancer Center Support grant no. P30CA016087 at the Laura and Isaac Perlmutter Cancer Center. Computing was partially supported by the Department of Scientific Computing at the Icahn School of Medicine at Mount Sinai. We acknowledge the contribution of the students who participated in obtaining the samples and the metadata: S.M. Rodriguez, J.F. Ruiz, N. Garcia and J.L. Rivera-Correa. We also thank M.J. Blaser for discussions and critical comments, and three anonymous reviewers for their suggestions to improve this manuscript.

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Affiliations

  1. School of Medicine, New York University, New York, New York, USA.

    • Maria G Dominguez-Bello
    • , Laura M Cox
    • , Nicholas A Bokulich
    •  & Marina Hoashi
  2. Department of Biology, University of Puerto Rico, Río Piedras Campus, San Juan, Puerto Rico, USA.

    • Maria G Dominguez-Bello
    •  & Kassandra M De Jesus-Laboy
  3. Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.

    • Nan Shen
    •  & Jose C Clemente
  4. Department of Pediatrics, University of California San Diego, La Jolla, California, USA.

    • Amnon Amir
    • , Antonio Gonzalez
    • , Se Jin Song
    •  & Rob Knight
  5. Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA.

    • Se Jin Song
  6. New York University Tandon School of Engineering, New York, New York, USA.

    • Marina Hoashi
  7. Department of Obstetrics and Gynecology, Medical Science Campus, University of Puerto Rico, San Juan, Puerto Rico, USA.

    • Juana I Rivera-Vinas
    •  & Keimari Mendez
  8. Department of Computer Science and Engineering, University of California San Diego, La Jolla, California, USA.

    • Rob Knight
  9. Department of Medicine, Division of Clinical Immunology, Icahn School of Medicine at Mount Sinai, New York, New York, USA.

    • Jose C Clemente

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Contributions

M.G.D.-B. designed the study. M.G.D.-B., K.M.D.J.-L., J.I.R.-V. and K.M. collected and processed specimens. M.G.D.-B. sequenced and generated data. N.S., L.M.C., A.A., A.G., N.A.B., S.J.S., M.H. and J.C.C. performed experiments. M.G.D.-B., N.S., L.M.C., A.A., A.G., N.A.B., S.J.S., M.H., R.K. and J.C.C. analyzed data. M.G.D.-B. and J.C.C. drafted the manuscript. All authors reviewed the final manuscript.

Competing interests

New York University has filed a US patent application (number 62161549) related to methods for restoring the microbiota of newborns on behalf of M.G.D.-B.

Corresponding authors

Correspondence to Maria G Dominguez-Bello or Jose C Clemente.

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DOI

https://doi.org/10.1038/nm.4039

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